As long as F1 and F2 do not interact, and it looks like they don't, then you can do this through a simple PARFOR loop. Something like the following would work.
matlabpool open 2
parfor i = 1:2
if i == 1
F1()
else
F2()
end
end
You can of course expand this with more loop iterations and other mechanisms like switch/case if you want the scripts to run more than once or add additional scripts into the loop.
However you need to keep in mind that with PARFOR you have no control over which loop iteration get run when and in what order. The above code opens 2 workers and has 2 loop iterations, so each iteration will be run at the same time on its own worker and will be run once. If you expand this to multiple runs of these functions or adding in more functions, then you may want to go the route of jobs and tasks to exercise more control.
